2WU1 - JenaLib

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Title :   GLUCOSAMINE-6-PHOSPHATE DEAMINASE COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOAMINE-6-PHOSPHATE BOTH IN THE ACTIVE AND ALLOSTERIC SITES.

Authors :   E. Rudino-Pinera, S. P. Rojas-Trejo, E. Horjales

Date :   25 Sep 09 (Deposition) - 06 Oct 09 (Release) - 06 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Allosteric Enzyme, Carbohydrate Metabolism, Aldose-Ketose Isomerase, Hydrolase, Disulfide Bond, Entropic Effects (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Rudino-Pinera, S. P. Rojas-Trejo, M. L. Calcagno, E. Horjales
Glucosamine-6-Phosphate Deaminase Mechanism: The Substrate Piranosic Ring Opening
To Be Published
PubMed: search

Molecule 1 - GLUCOSAMINE-6-PHOSPHATE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.99.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTZ18-R
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	GLUCOSAMINE-6-PHOSPHATE ISOMERASE, GLCN6P DEAMINASE, GNPDA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	16G	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	FGS	2	Ligand/Ion	5-(ACETYLAMINO)-5-DEOXY-1-O-PHOSPHONO-L-IDITOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	16G	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	FGS	1	Ligand/Ion	5-(ACETYLAMINO)-5-DEOXY-1-O-PHOSPHONO-L-IDITOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	16G	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	FGS	1	Ligand/Ion	5-(ACETYLAMINO)-5-DEOXY-1-O-PHOSPHONO-L-IDITOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:1 , SER A:151 , SER A:152 , ARG A:158 , ILE A:159 , LYS A:160 , THR A:161 , HOH A:2069 , HOH A:2098 , HOH A:2113 , HOH A:2115 , HOH A:2116 , HOH A:2117	BINDING SITE FOR RESIDUE 16G A1267
2	AC2	SOFTWARE	MET B:301 , SER B:451 , SER B:452 , ARG B:458 , ILE B:459 , LYS B:460 , THR B:461 , HOH B:2131 , HOH B:2132 , HOH B:2133 , HOH B:2134 , HOH B:2135 , HOH B:2136	BINDING SITE FOR RESIDUE 16G B1567
3	AC3	SOFTWARE	GLY A:43 , THR A:44 , VAL A:138 , GLY A:139 , ASN A:140 , HIS A:143 , PHE A:146 , THR A:166 , ALA A:169 , ASN A:170 , ARG A:172 , LYS A:208 , HOH A:2119	BINDING SITE FOR RESIDUE FGS A1268
4	AC4	SOFTWARE	GLY B:342 , GLY B:343 , THR B:344 , VAL B:438 , GLY B:439 , ASN B:440 , HIS B:443 , PHE B:446 , THR B:466 , ALA B:469 , ASN B:470 , ARG B:472 , LYS B:508	BINDING SITE FOR RESIDUE FGS B1568

(no "SS Bond" information available for 2WU1)

Asymmetric Unit

No.	Residues
1	Lys A:264	-	Gly A:265

(no "SAP(SNP)/Variant" information available for 2WU1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	2	A:125-143 B:425-443

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	1	A:125-143 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	1	- B:425-443

(no "Exon" information available for 2WU1)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d2wu1a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2wu1A00 A:1-266  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........hhhhhhhhhhhhhhh......eee.......hhhhhhhhhhhhhh.......eeee..eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhh.............................eeee.hhhhhhhhhhhh..hhhhh..eeee...........eeeee....hhhhhhhhhh......hhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wu1 A   1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d2wu1b_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2wu1B00 B:301-566  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) -----------Glucosamine_iso-2wu1B01 B:312-517                                                                                                                                                                             ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Glucosamine_iso-2wu1B02 B:312-517                                                                                                                                                                             ------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee........hhhhhhhhhhhhhhh......eee.......hhhhhhhhhhhhhh.......eeee..eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhh.............................eeee.hhhhhhhhhhhh..hhhhh..eeee...........eeeee....hhhhhhhhhh......hhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wu1 B 301 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 566
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: NagB/RpiA/CoA transferase-like (94)

Superfamily: NagB/RpiA/CoA transferase-like (94)

Family: NagB-like (14)

Protein domain: automated matches (1)

Escherichia coli K-12 [TaxId: 83333] (1)

1a	d2wu1a_	A:
1b	d2wu1b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1360, no name defined] (40)

Escherichia coli. Organism_taxid: 83333. Strain: k-12. (1)

1a	2wu1A00	A:1-266
1b	2wu1B00	B:301-566

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ISOCOT_Fold (53)

Family: Glucosamine_iso (12)

Escherichia coli (strain K12) (2)

1a	Glucosamine_iso-2wu1B01	B:312-517
1b	Glucosamine_iso-2wu1B02	B:312-517

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAGB_ECOLI | P0A759)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004342	glucosamine-6-phosphate deaminase activity	Catalysis of the reaction: D-glucosamine 6-phosphate + H(2)O = beta-D-fructose 6-phosphate + NH(4)(+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	GO:0006046	N-acetylglucosamine catabolic process	The chemical reactions and pathways resulting in the breakdown of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	GO:0006044	N-acetylglucosamine metabolic process	The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	GO:0019262	N-acetylneuraminate catabolic process	The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
	GO:0006048	UDP-N-acetylglucosamine biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:264 - Gly A:265	[ RasMol ]

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	2wu1
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	3.5.99.6
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UniProtKB/Swiss-Prot
	NAGB_ECOLI \| P0A759	:	1cd5 1dea 1fqo 1frz 1fs5 1fs6 1fsf 1hor 1hot 1jt9

1cd5	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E. COLI, T CONFORMER
1dea
1fqo	GLUCOSAMINE 6-PHOSPHATE DEAMINASE COMPLEXED WITH THESUBSTRATE OF THE REVERSE REACTION FRUCTOSE 6-PHOSPHATE(OPEN FORM)
1frz	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E. COLI, R CONFORMER.COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6- PHOSPHATE AT 2.2 A RESOLUTION
1fs5	A DISCOVERY OF THREE ALTERNATE CONFORMATIONS IN THE ACTIVESITE OF GLUCOSAMINE-6-PHOSPHATE ISOMERASE
1fs6	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E. COLI, T CONFORMER,AT 2.2A RESOLUTION
1fsf	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E. COLI, T CONFORMER,AT 1.9A RESOLUTION
1hor
1hot	GLUCOSAMINE 6-PHOSPHATE DEAMINASE COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL- GLUCOSAMINE-6-PHOSPHATE
1jt9	STRUCTURE OF THE MUTANT F174A T FORM OF THE GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E .COLI

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (0, 0)

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